|
Status |
Public on Feb 04, 2013 |
Title |
HU_WT_RNAseq_rep2 |
Sample type |
SRA |
|
|
Source name |
Splenic B Cells
|
Organism |
Mus musculus |
Characteristics |
cell type: In vitro activated B Cells strain: 129/Sv x C57BL/6 genotype: wildtype growth duration: 28 hr treatment protocol: 10 mM hydroxyurea for 6 hrs
|
Growth protocol |
CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech). Following isolation, resting B cells were stimulated with LPS (25 mcg/ml, Sigma) and IL-4 (5 ng/ml, Sigma) for 28 hrs.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using TRIzol (Ambion) following manufacturer's protocol. RNA was washed, purified using RNeasy kit (Qiagen), and measured for quality. RNA was then prepared for sequencing using the TruSeq RNA sample prep kit (Illumina). Four libraries were sequenced on one lane of HiSeq 2000.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Illumina Casava1.7.0 or 1.8.0 software used for basecalling. Genome_build: mm9 RNA-Seq sequenced reads were mapped to mm9 using Tophat v2.0.6. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using exons of each transcript annotated by BioConductor's GenomicFeatures 1.10.1.
|
|
|
Submission date |
Jan 15, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Robert Babak Faryabi |
E-mail(s) |
[email protected]
|
Phone |
215-573-8220
|
Organization name |
University of Pennsylvania
|
Department |
Pathology
|
Lab |
Faryabi Lab
|
Street address |
Room 553 BRB II/III, 421 Curie Boulevard
|
City |
Philadelphia |
State/province |
Pennsylvania |
ZIP/Postal code |
19104 |
Country |
USA |
|
|
Platform ID |
GPL13112 |
Series (1) |
GSE43504 |
Genome-wide mapping of early replication fragile sites (ERFS) |
|
Relations |
SRA |
SRX217136 |
BioSample |
SAMN01886668 |